In any particular geographic area, whether aquatic or land, it is often desirable to determine in a population of plants the genotype of those plants. A particular challenge is when in a population of plants there exists more than one species of a genus of the plant, where one or more species has a characteristic distinct from the other, yet is morphologically indistinct. An example of such a situation is where within a population of plants, the wild type species is inter-planted with another species that is more aggressive, more resistant to herbicide application, or has another undesirable characteristic. This is complicated further when the species interbreed, producing a hybrid.
An example is watermilfoil plants of the genus Myriophyllum. The invasive aquatic plant Eurasian watermilfoil (Myriophyllum spicatum L.) readily hybridizes with the related North American native species northern watermilfoil (M. sibiricum Kom.). Hybrid watermilfoil (M. spicatum×M. sibiricum) populations have higher fitness and reduced sensitivity to some commonly used herbicides, making management more difficult. There is growing concern that management practices using herbicides with mixed populations such as watermilfoil species may further select for hybrid individuals due to the difference in herbicide sensitivity. Accurate and cost-effective identification of hybrid individuals within populations is therefore critical for management decisions.
Still another example are the land plants of the genus Amaranthus. Palmer amaranth (Amaranthus palmeri) and waterhemp (Amaranthus tuberculatus) are important weed species that can contaminate seeds for sale (e.g., wildflowers, native grasses). Palmer amaranth has been listed as a prohibited noxious weed species in some US states, meaning that a seed lot containing Palmer amaranth may not legally be sold. Waterhemp is prohibited from seeds for sale in Canada and China. Waterhemp and Palmer amaranth seeds cannot be distinguished visually from other, non-noxious Amaranthus species, such as redroot pigweed (Amaranthus retroflexus), smooth pigweed (Amaranthus hybridus), and spiny amaranth (Amaranthus spinosus). There is no fast and inexpensive method for the seed testing industry to reliably assess bulked amaranth seed samples as containing Palmer amaranth or not. Therefore, the seed production and analysis industry has considerable interest in a DNA-based test to identify the presence of any Palmer amaranth and waterhemp seeds.